Nelson left LucasArts in 1998 to join the effects team at ILM where he was a compositor, rotoscoper, matte painter, and texture artist. His work at ILM includes Star Wars: Episode I The Phantom Menace, Galaxy Quest, The Adventures of Rocky & Bullwinkle, The Perfect Storm, Jurassic Park III, The Time Machine, and Star Wars: Episode II Attack of the Clones. After the completion of Episode II, Nelson joined the full-time faculty of the Academy of Art University and served as the school's Visual Effects Director from 2002 to 2004. He currently consults for various leading effects and animation studios. He is a member of the Visual Effects Society.

It is a common misunderstanding on part of the media that during Star Wars: Rebel Assault II: The Hidden Empire production Vader was played by David Prowse reprising his legendary role. As Nelson says, he feels it's a great honor that some mistook him for Prowse. In many appearances that C. Andrew Nelson made as Darth Vader, his voice was dubbed over by voice-actor Scott Lawrence who plays Vader as a voice-actor in a dozen Star Wars video games. Nelson also voiced Luke Skywalker for a cutscene of the Star Wars: X-Wing expansion pack, being the first actor to have ever officially played both Darth Vader and Luke Skywalker.

He continues to act in feature films, television, commercials, and voice-over.